From the macro Man-start-callingto man.el:
(let (...
(default-directory
(if (and (file-directory-p default-directory)
(not (find-file-name-handler default-directory
'file-directory-p)))
default-directory
"/"))
That is, if there is a special file name handler for the current default directory, such as Tramp, it will use the root directory as the directory to run manfrom from, and therefore it will see man pages from the system that Emacs is running.
It seems that there is no way to disable this, except for the change man.el. Note that this is a macro, so you need to reload the macro and all the functions that use the macro.
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